Engineering microbial consortia with rationally designed cellular interactions

Abstract

Synthetic microbial consortia represent a frontier of synthetic biology that promises versatile engineering of cellular functions. They are primarily developed through the design and construction of cellular interactions that coordinate individual dynamics and generate collective behaviors. Here we review recent advances in the engineering of synthetic communities through cellular-interaction programming. We first examine fundamental building blocks for intercellular communication and unidirectional positive and negative interactions. We then recap the assembly of the building blocks for creating bidirectional interactions in two-species ecosystems, which is followed by the discussion of engineering toward complex communities with increasing species numbers, under spatial contexts, and via model-guided design. We conclude by summarizing major challenges and future opportunities of engineered microbial ecosystems.

Figure 1

Simple cellular interactions as building blocks. (a) Unidirectional signaling enables intercellular communication by the production and response of signaling molecules. (b) Quorum sensing relies on positive self-feedback to coordinate population behaviors. (c) Negative interactions can be realized through direct release of toxic molecules. (d) Negative interactions can be fulfilled by intercellular signaling-triggered production of toxins. (e) Positive interactions can be established through direct secretion of beneficial substances. (f) Positive interactions can arise from communication-mediated induction of genes encoding beneficial molecules. P_con indicates a promoter with constitutive expression. P_qsi indicates a promoter regulated by signaling molecules.

Figure 2

Creation of bidirectional interactions in two-species communities. Assembly of unidirectional positive and negative interactions with opposite directions can result in two-species consortia with cooperation (a), competition (b), or predation (c).

Figure 3

Synthetic microbial consortia with increased complexity. (a) A synthetic three-strain consortium built with cyclic negative interactions using three toxin–antitoxin pathways [12]. (b) A stable five-strain consortium driven primarily by positive interactions mediated by syntrophic amino-acid exchanges [13]. (c) Engineered four-strain community involving mixtures of positive and cooperative interactions [64]. (d) A two-species community that utilizes AHL-mediated positive and negative feedback, yields synchronized-system dynamics in a spatially extended microfluidic trap [56]. (e) A competitive consortium, which includes contact-dependent short-range inhibition and communication-mediated, long-range inhibition, produces divergent spatial colony structures when grown on agar plates [16]. (f) A three-strain consortium that employs protein-synthesis inhibition, genomic DNA digestion, and cell-membrane disruption for cyclic negative interactions. With an even initial distribution of the three strains on agar plates, the growth of the consortium resulted in the survival of the strain with the weakest competitive advantage [12]. P_con indicates a promoter with constitutive expression. All other promoters are regulated by signaling molecules as indicated.